Question: Aachanges / Bed-To-Codon
0
Christopher Schroeder • 20 wrote:
Hello list,
I already analysed some of our data with your framework and I want to
thank
you for your great work. But lately I stumbled on some strange
behavior - I
used the "aaChanges"-tool, as well as the Gene "BED-to-Codon"-tool
with the
same Gene-BED-File and compared the results. What I did:
#example BED-file:
chr17 3763624 3794037 uc002fwt.2 0 - 3765504 3788981
0
16 1953,104,129,88,74,54,200,89,22,37,134,52,54,48,403,51,
0,5577,9156,9470,12223,13078,15892,20015,21296,22197,22711,23098,23553
,24049
,24997,30362,
#example-output of "aaChanges"
chr17 3775847 3775848 C uc002fwt.2 Glu:Gly 375 T
#example-output of "BED-to-Codon"
chr17 3773172 3773175 uc002fwt.2 0 -
chr17 3773175 3773178 uc002fwt.2 0 -
chr17 3773178 3773181 uc002fwt.2 0 -
chr17 3775849 3775852 uc002fwt.2 0 -
chr17 3775852 3775855 uc002fwt.2 0 -
Comparing both results, the "BED-to-Codon" actually presents no codon
at
position 3775848 - here the fist codon is starting at 3775849. But in
fact,
looking at the ucsc browser, "aaChanges" is right. There are another
few
examples (~5/1500 snps) and apparently most of them are positions
among the
first codon in an exon.
Did anyone meet this problem before? What is my mistake?
Thank you.
Regards
Chris
ADD COMMENT
• link
•
modified 7.7 years ago
by
Jennifer Hillman Jackson ♦ 25k
•
written
7.7 years ago by
Christopher Schroeder • 20
